a.

AA sequence: RTGVGTHLTSLALPGKAEGVASLTSQCSYSSTIVHVGDKKP

b.

1 ~~mehvafgsedientlakmddgqldglafGAIQLDGDGNILQYNAAEGd~~iTGRDPKQ 56 3PYP
1 ~~~~~~~~~~~~~~~mrethlrsilhtipdAMIVIDGHGIIQLFSTAAEr~~lFGWSELE 43 1DRM_A
 
57 VIGKNFfkDVAPCTDspeFYGKFKEGvas~~~~gnlNTMF~EYTFDYQ~MTPTKVKVHMK 110 3PYP
44 AIGQNVn~ILMPEPDrsrHDSYISRYrttsd~phiiGIGR~IVTGKRRdGTTFPMHLSIG 100 1DRM_A
 
111 Kals~~~~~~gdsYWVFVKRV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 3PYP
101 Emqsg~~~~gepyFTGFVRDLtehqqtqarlqelq~~~~~~~~~~~~~~~~~~~~~~~~ 131 1DRM_A

Figure 2: Alignment of two amino acid sequences retrieved from a protein-protein Blast search at NCBI used in Activity 1. A.) is the starting amino acid sequence for a portion of the Period 2 protein. B.) 3PYP is the sequence retrieved from the database that has the most similarity with the target amino acid sequence. 1DRM A is the heme domain of a protein from the bacterium, Bradyrhizobium japonicum that has putative homology with 3PYP. These two proteins have been aligned side by side to aid in a pair wise comparison. The capital letters were determined by NCBI’s protein homology algorithm to be the most chemically similar amino acids and have putative structural homology.

Follows the steps for visualizing the superimposed 3-D crystalline models of 3PYP and 1DRM A. Then answer the following:

• From the pair wise comparison of AA’s in both sequences do you think these are homologous proteins? Why or why not?
• After seeing the 3-D models, do you think 3PYP and 1DRM A are homologous proteins? Do you think they have a similar function?
• What evidence would lead you to believe two amino acid sequences are homologous?